6-134982499-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_006620.4(HBS1L):c.1556G>A(p.Arg519Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000158 in 1,459,148 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006620.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HBS1L | NM_006620.4 | c.1556G>A | p.Arg519Gln | missense_variant | Exon 13 of 18 | ENST00000367837.10 | NP_006611.1 | |
HBS1L | NM_001145158.2 | c.1430G>A | p.Arg477Gln | missense_variant | Exon 12 of 17 | NP_001138630.1 | ||
HBS1L | NM_001363686.2 | c.1064G>A | p.Arg355Gln | missense_variant | Exon 14 of 19 | NP_001350615.1 | ||
HBS1L | XM_047418093.1 | c.1556G>A | p.Arg519Gln | missense_variant | Exon 13 of 16 | XP_047274049.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250428Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135326
GnomAD4 exome AF: 0.0000158 AC: 23AN: 1459148Hom.: 0 Cov.: 28 AF XY: 0.0000110 AC XY: 8AN XY: 725952
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1556G>A (p.R519Q) alteration is located in exon 13 (coding exon 13) of the HBS1L gene. This alteration results from a G to A substitution at nucleotide position 1556, causing the arginine (R) at amino acid position 519 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at